A variety of nucleic acid amplification assays and immunological assays are used for analysis of cells and nucleic acids. These assays can be used to detect or characterize nucleic acid sequences associated with particular diseases or genetic disorders, for genotyping, for gene expression analyses, to detect and identify pathogens such as viruses, bacteria and fungi), for paternity and forensic identification, and for many other purposes. However, in some applications the efficiency and sensitivity of these assays is reduced, which may render the assays useless or at minimum require that additional manipulations and/or significant amounts of expensive reagents be used. For example, when a cell or molecule to be analyzed is from a sample with a large excess of non-target cells or molecules (e.g., as in genetic or phenotypic analysis of a rare cell in a background of other cells) conventional assay methods are inadequate. Similarly, when a number of different targets must be detected in a single sample, conventional approaches (e.g., multiplex PCR) are expensive, inefficient or not sufficiently sensitive. Thus, new methods, reagents and devices for detection and characterization of nucleic acids, cells, and other biological molecules will find broad application in biomedicine and other fields.